QBiC

Project Members:

Prof. Dr. Verena Keitel

verena.keitel@med.uni-duesseldorf.de

Universitätsklinikum Düsseldorf


Dr. Maria Reich

maria.reich@uni-duesseldorf.de

Universitätsklinikum Düsseldorf


Prof. Dr. Mathias Heikenwälder

m.heikenwaelder@dkfz-heidelberg.de

DKFZ Heidelberg




QBiC contacts:

Dr. Gisela Gabernet

Bioinformatics project manager

gisela.gabernet@qbic.uni-tuebingen.de

1 Pathway analysis

The pathway analysis results are stored under results/pathway_analysis, and explained in this section.

1.1 Enriched pathways plot

The plot below summarizes the pathways that were found significantly enriched in DE genes for each contrast (padj value < 0.05). Only contrasts for which an enriched pathway was found are shown. Both KEGG pathways and REACTOME (REAC) pathways were considered.

Hover over the dots to reveal the pathway names.

1.2 Enriched pathways table

Table summarizing all the enriched pathways. The results can also be inspected on the browser query under this link: https://biit.cs.ut.ee/gplink/l/WvtPn1HzTm. This table can be also found under results/pathway_analysis.

Contrast Pathway name Pathway code DE genes in pathway (N) Total genes in pathway (N) Fraction of DE genes in pathway Padj value (pathway enrichment) DE genes names
DE_genes_Cholangiocytes_TGR5_vs_MDR2KO Innate Immune System REAC:R-MMU-168249 11 976 0.0113 0.0441 Hspa8,Pigr,Dynll1,Actg1,Txnip,Dsp,Ubc,Ahsg,Lcn2,Vtn,Cxcl1
DE_genes_Endothelial_TGR5_vs_MDR2KO Type I diabetes mellitus KEGG:04940 10 62 0.161 9.9e-11 H2-D1,H2-K1,H2-Q6,H2-T23,H2-Q7,Il1b,Cpe,H2-Eb1,H2-Aa,H2-Ab1
DE_genes_Endothelial_TGR5_vs_MDR2KO Graft-versus-host disease KEGG:05332 9 55 0.164 1.27e-09 H2-D1,H2-K1,H2-Q6,H2-T23,H2-Q7,Il1b,H2-Eb1,H2-Aa,H2-Ab1
DE_genes_Endothelial_TGR5_vs_MDR2KO Antigen processing and presentation KEGG:04612 10 81 0.123 1.6e-09 H2-D1,H2-K1,B2m,H2-Q6,H2-T23,H2-Q7,H2-Eb1,Cd74,H2-Aa,H2-Ab1
DE_genes_Endothelial_TGR5_vs_MDR2KO Allograft rejection KEGG:05330 8 55 0.145 4.98e-08 H2-D1,H2-K1,H2-Q6,H2-T23,H2-Q7,H2-Eb1,H2-Aa,H2-Ab1
DE_genes_Endothelial_TGR5_vs_MDR2KO Autoimmune thyroid disease KEGG:05320 8 70 0.114 3.62e-07 H2-D1,H2-K1,H2-Q6,H2-T23,H2-Q7,H2-Eb1,H2-Aa,H2-Ab1
DE_genes_Endothelial_TGR5_vs_MDR2KO Viral myocarditis KEGG:05416 8 80 0.1 1.06e-06 H2-D1,H2-K1,H2-Q6,H2-T23,H2-Q7,H2-Eb1,H2-Aa,H2-Ab1
DE_genes_Endothelial_TGR5_vs_MDR2KO Epstein-Barr virus infection KEGG:05169 11 221 0.0498 2.63e-06 H2-D1,H2-K1,B2m,H2-Q6,H2-T23,H2-Q7,Gadd45b,Jun,H2-Eb1,H2-Aa,H2-Ab1
DE_genes_Endothelial_TGR5_vs_MDR2KO Phagosome KEGG:04145 10 173 0.0578 2.92e-06 H2-D1,H2-K1,H2-Q6,H2-T23,H2-Q7,C3,H2-Eb1,H2-Aa,H2-Ab1,Fcgr2b
DE_genes_Endothelial_TGR5_vs_MDR2KO Cell adhesion molecules KEGG:04514 9 162 0.0556 2.13e-05 H2-D1,H2-K1,H2-Q6,H2-T23,H2-Q7,Alcam,H2-Eb1,H2-Aa,H2-Ab1
DE_genes_Endothelial_TGR5_vs_MDR2KO Human T-cell leukemia virus 1 infection KEGG:05166 10 236 0.0424 5.36e-05 H2-D1,H2-K1,B2m,H2-Q6,H2-T23,H2-Q7,Jun,H2-Eb1,H2-Aa,H2-Ab1
DE_genes_Endothelial_TGR5_vs_MDR2KO Leishmaniasis KEGG:05140 6 70 0.0857 0.000197 Il1b,C3,Jun,H2-Eb1,H2-Aa,H2-Ab1
DE_genes_Endothelial_TGR5_vs_MDR2KO Staphylococcus aureus infection KEGG:05150 7 116 0.0603 0.000293 C1qb,C3,H2-Eb1,C1qa,H2-Aa,H2-Ab1,Fcgr2b
DE_genes_Endothelial_TGR5_vs_MDR2KO Herpes simplex virus 1 infection KEGG:05168 12 436 0.0275 0.00035 H2-D1,H2-K1,B2m,H2-Q6,H2-T23,H2-Q7,Il1b,C3,H2-Eb1,Cd74,H2-Aa,H2-Ab1
DE_genes_Endothelial_TGR5_vs_MDR2KO Coronavirus disease - COVID-19 KEGG:05171 9 239 0.0377 0.000544 Rpl37a,Rps29,Rps18,Rps2,Il1b,C1qb,C3,Jun,C1qa
DE_genes_Endothelial_TGR5_vs_MDR2KO Rheumatoid arthritis KEGG:05323 6 84 0.0714 0.000576 Il1b,Cxcl2,Jun,H2-Eb1,H2-Aa,H2-Ab1
DE_genes_Endothelial_TGR5_vs_MDR2KO Inflammatory bowel disease KEGG:05321 5 61 0.082 0.00179 Il1b,Jun,H2-Eb1,H2-Aa,H2-Ab1
DE_genes_Endothelial_TGR5_vs_MDR2KO Kaposi sarcoma-associated herpesvirus infection KEGG:05167 8 217 0.0369 0.00217 H2-D1,H2-K1,H2-Q6,H2-T23,H2-Q7,Cxcl2,C3,Jun
DE_genes_Endothelial_TGR5_vs_MDR2KO Tuberculosis KEGG:05152 7 179 0.0391 0.00495 Il1b,C3,H2-Eb1,Cd74,H2-Aa,H2-Ab1,Fcgr2b
DE_genes_Endothelial_TGR5_vs_MDR2KO Pertussis KEGG:05133 5 76 0.0658 0.0052 Il1b,C1qb,C3,Jun,C1qa
DE_genes_Endothelial_TGR5_vs_MDR2KO Systemic lupus erythematosus KEGG:05322 6 141 0.0426 0.0108 C1qb,C3,H2-Eb1,C1qa,H2-Aa,H2-Ab1
DE_genes_Endothelial_TGR5_vs_MDR2KO Viral carcinogenesis KEGG:05203 7 216 0.0324 0.016 H2-D1,H2-K1,H2-Q6,H2-T23,H2-Q7,C3,Jun
DE_genes_Endothelial_TGR5_vs_MDR2KO Chagas disease KEGG:05142 5 102 0.049 0.021 Il1b,C1qb,C3,Jun,C1qa
DE_genes_Endothelial_TGR5_vs_MDR2KO Th17 cell differentiation KEGG:04659 5 103 0.0485 0.0219 Il1b,Jun,H2-Eb1,H2-Aa,H2-Ab1
DE_genes_Endothelial_TGR5_vs_MDR2KO Human immunodeficiency virus 1 infection KEGG:05170 7 228 0.0307 0.0223 H2-D1,H2-K1,B2m,H2-Q6,H2-T23,H2-Q7,Jun
DE_genes_Endothelial_TGR5_vs_MDR2KO Asthma KEGG:05310 3 25 0.12 0.0279 H2-Eb1,H2-Aa,H2-Ab1
DE_genes_Endothelial_TGR5_vs_MDR2KO Cellular senescence KEGG:04218 6 171 0.0351 0.0308 H2-D1,H2-K1,H2-Q6,H2-T23,H2-Q7,Gadd45b
DE_genes_Endothelial_TGR5_vs_MDR2KO Human cytomegalovirus infection KEGG:05163 7 245 0.0286 0.0345 H2-D1,H2-K1,B2m,H2-Q6,H2-T23,H2-Q7,Il1b
DE_genes_Endothelial_TGR5_vs_MDR2KO Endosomal/Vacuolar pathway REAC:R-MMU-1236977 5 29 0.172 9.43e-05 H2-K1,B2m,H2-Q6,H2-T23,H2-Q7
DE_genes_Endothelial_TGR5_vs_MDR2KO DAP12 signaling REAC:R-MMU-2424491 6 55 0.109 9.85e-05 H2-K1,B2m,H2-Q6,H2-T23,H2-Q7,Tyrobp
DE_genes_Endothelial_TGR5_vs_MDR2KO DAP12 interactions REAC:R-MMU-2172127 6 64 0.0938 0.000246 H2-K1,B2m,H2-Q6,H2-T23,H2-Q7,Tyrobp
DE_genes_Endothelial_TGR5_vs_MDR2KO ER-Phagosome pathway REAC:R-MMU-1236974 5 37 0.135 0.000335 H2-K1,B2m,H2-Q6,H2-T23,H2-Q7
DE_genes_Endothelial_TGR5_vs_MDR2KO Antigen Presentation: Folding, assembly and peptide loading of class I MHC REAC:R-MMU-983170 5 45 0.111 0.000911 H2-K1,B2m,H2-Q6,H2-T23,H2-Q7
DE_genes_Endothelial_TGR5_vs_MDR2KO Post-translational protein phosphorylation REAC:R-MMU-8957275 6 105 0.0571 0.00448 Spp1,Prss23,Apoe,C3,Lgals1,Ccn1
DE_genes_Endothelial_TGR5_vs_MDR2KO Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) REAC:R-MMU-381426 6 111 0.0541 0.00616 Spp1,Prss23,Apoe,C3,Lgals1,Ccn1
DE_genes_Endothelial_TGR5_vs_MDR2KO Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell REAC:R-MMU-198933 7 177 0.0395 0.0093 H2-K1,B2m,H2-Q6,H2-T23,H2-Q7,Cd300lg,C3
DE_genes_Endothelial_TGR5_vs_MDR2KO Innate Immune System REAC:R-MMU-168249 15 976 0.0154 0.0239 H2-K1,B2m,H2-Q6,H2-T23,H2-Q7,Cd93,Il1b,Clu,Lyz2,C1qb,Cxcl2,C3,Jun,Tyrobp,C1qa
DE_genes_Endothelial_TGR5_vs_MDR2KO Antigen processing-Cross presentation REAC:R-MMU-1236975 5 95 0.0526 0.0355 H2-K1,B2m,H2-Q6,H2-T23,H2-Q7
DE_genes_Endothelial_vascular_TGR5_vs_MDR2KO Human T-cell leukemia virus 1 infection KEGG:05166 9 236 0.0381 0.00334 H2-D1,Fos,H2-K1,Icam1,Jun,H2-Q7,Ccnd2,Egr1,Zfp36
DE_genes_Endothelial_vascular_TGR5_vs_MDR2KO Fluid shear stress and atherosclerosis KEGG:05418 7 141 0.0496 0.00493 Gstm1,Fos,Icam1,Jun,Ass1,Dusp1,Klf2
DE_genes_Endothelial_vascular_TGR5_vs_MDR2KO Kaposi sarcoma-associated herpesvirus infection KEGG:05167 8 217 0.0369 0.0117 H2-D1,Fos,H2-K1,Icam1,Jun,Lyn,H2-Q7,Zfp36
DE_genes_Endothelial_vascular_TGR5_vs_MDR2KO Scavenging by Class H Receptors REAC:R-MMU-3000497 2 3 0.667 0.0425 Sparc,Stab2
DE_genes_Fibroblasts_TGR5_vs_MDR2KO Antigen processing and presentation KEGG:04612 4 81 0.0494 0.00934 B2m,H2-D1,H2-K1,Cd74
DE_genes_Hepatocytes_TGR5_vs_MDR2KO Metabolic pathways KEGG:01100 25 1531 0.0163 0.000128 Scd1,Aox3,Car3,Elovl3,Glud1,Nnmt,Hsd3b5,Hpd,Uox,Ugp2,Acat1,Got1,Ephx2,Gapdh,Acaa1b,Selenbp2,Me1,Sds,mt-Nd4l,Gstm3,mt-Nd5,Ptgds,Cyp2c29,Cyp2e1,Glul
DE_genes_Hepatocytes_TGR5_vs_MDR2KO Carbon metabolism KEGG:01200 6 123 0.0488 0.0094 Glud1,Acat1,Got1,Gapdh,Me1,Sds
DE_genes_Hepatocytes_TGR5_vs_MDR2KO Nitrogen metabolism KEGG:00910 3 17 0.176 0.0121 Car3,Glud1,Glul
DE_genes_Hepatocytes_TGR5_vs_MDR2KO PPAR signaling pathway KEGG:03320 5 89 0.0562 0.0187 Scd1,Fabp1,Ubc,Acaa1b,Me1
DE_genes_Hepatocytes_TGR5_vs_MDR2KO Arginine biosynthesis KEGG:00220 3 20 0.15 0.0201 Glud1,Got1,Glul
DE_genes_Hepatocytes_TGR5_vs_MDR2KO Complement and coagulation cascades KEGG:04610 5 91 0.0549 0.0208 F12,Serpina1e,Clu,Vtn,C3
DE_genes_Hepatocytes_TGR5_vs_MDR2KO Fatty acid metabolism KEGG:01212 4 62 0.0645 0.0486 Scd1,Elovl3,Acat1,Acaa1b
DE_genes_Hepatocytes_TGR5_vs_MDR2KO Platelet degranulation REAC:R-MMU-114608 8 110 0.0727 0.000141 Rarres2,Ahsg,Cd63,A1bg,Tagln2,Clu,Anxa5,Actg1
DE_genes_Hepatocytes_TGR5_vs_MDR2KO Response to elevated platelet cytosolic Ca2+ REAC:R-MMU-76005 8 115 0.0696 0.000199 Rarres2,Ahsg,Cd63,A1bg,Tagln2,Clu,Anxa5,Actg1
DE_genes_Hepatocytes_TGR5_vs_MDR2KO Metabolism REAC:R-MMU-1430728 26 1678 0.0155 0.00152 Scd1,Fabp1,Car3,Elovl3,Glud1,Akr1c19,Nnmt,Hsd3b5,Hpd,Ugp2,Rbp4,Acat1,Got1,Ephx2,Gapdh,Thrsp,Me1,Bsg,Fitm1,Sds,Apom,mt-Nd5,Serpina6,Ptgds,Cyp2e1,Glul
DE_genes_Hepatocytes_TGR5_vs_MDR2KO Post-translational protein phosphorylation REAC:R-MMU-8957275 6 105 0.0571 0.0166 Ahsg,Spp1,Ccn1,Mfge8,Cp,C3
DE_genes_Hepatocytes_TGR5_vs_MDR2KO Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) REAC:R-MMU-381426 6 111 0.0541 0.0227 Ahsg,Spp1,Ccn1,Mfge8,Cp,C3
DE_genes_Hepatocytes_TGR5_vs_MDR2KO Platelet activation, signaling and aggregation REAC:R-MMU-76002 8 239 0.0335 0.0421 Rarres2,Ahsg,Cd63,A1bg,Tagln2,Clu,Anxa5,Actg1
DE_genes_HSC_TGR5_vs_MDR2KO Antigen processing and presentation KEGG:04612 8 81 0.0988 7.15e-07 B2m,H2-D1,H2-K1,Hspa1a,Cd74,H2-Aa,H2-Eb1,H2-Ab1
DE_genes_HSC_TGR5_vs_MDR2KO Staphylococcus aureus infection KEGG:05150 7 116 0.0603 0.000194 Krt18,H2-Aa,H2-Eb1,H2-Ab1,C1qb,C1qa,C1qc
DE_genes_HSC_TGR5_vs_MDR2KO Complement and coagulation cascades KEGG:04610 6 91 0.0659 0.000646 Clu,F3,C7,C1qb,C1qa,C1qc
DE_genes_HSC_TGR5_vs_MDR2KO Systemic lupus erythematosus KEGG:05322 7 141 0.0496 0.00071 C7,H2-Aa,H2-Eb1,H2-Ab1,C1qb,C1qa,C1qc
DE_genes_HSC_TGR5_vs_MDR2KO Graft-versus-host disease KEGG:05332 5 55 0.0909 0.000804 H2-D1,H2-K1,H2-Aa,H2-Eb1,H2-Ab1
DE_genes_HSC_TGR5_vs_MDR2KO Allograft rejection KEGG:05330 5 55 0.0909 0.000804 H2-D1,H2-K1,H2-Aa,H2-Eb1,H2-Ab1
DE_genes_HSC_TGR5_vs_MDR2KO Type I diabetes mellitus KEGG:04940 5 62 0.0806 0.00145 H2-D1,H2-K1,H2-Aa,H2-Eb1,H2-Ab1
DE_genes_HSC_TGR5_vs_MDR2KO Autoimmune thyroid disease KEGG:05320 5 70 0.0714 0.00263 H2-D1,H2-K1,H2-Aa,H2-Eb1,H2-Ab1
DE_genes_HSC_TGR5_vs_MDR2KO Viral myocarditis KEGG:05416 5 80 0.0625 0.00502 H2-D1,H2-K1,H2-Aa,H2-Eb1,H2-Ab1
DE_genes_HSC_TGR5_vs_MDR2KO Prion disease KEGG:05020 8 261 0.0307 0.00516 mt-Nd4l,mt-Nd5,mt-Nd3,C7,Hspa1a,C1qb,C1qa,C1qc
DE_genes_HSC_TGR5_vs_MDR2KO Rheumatoid arthritis KEGG:05323 5 84 0.0595 0.00635 Jun,Mmp3,H2-Aa,H2-Eb1,H2-Ab1
DE_genes_HSC_TGR5_vs_MDR2KO Epstein-Barr virus infection KEGG:05169 7 221 0.0317 0.0126 B2m,H2-D1,H2-K1,Jun,H2-Aa,H2-Eb1,H2-Ab1
DE_genes_HSC_TGR5_vs_MDR2KO Human T-cell leukemia virus 1 infection KEGG:05166 7 236 0.0297 0.0189 B2m,H2-D1,H2-K1,Jun,H2-Aa,H2-Eb1,H2-Ab1
DE_genes_HSC_TGR5_vs_MDR2KO Coronavirus disease - COVID-19 KEGG:05171 7 239 0.0293 0.0204 Rps2,Jun,C7,Mmp3,C1qb,C1qa,C1qc
DE_genes_HSC_TGR5_vs_MDR2KO Inflammatory bowel disease KEGG:05321 4 61 0.0656 0.0238 Jun,H2-Aa,H2-Eb1,H2-Ab1
DE_genes_HSC_TGR5_vs_MDR2KO Asthma KEGG:05310 3 25 0.12 0.0238 H2-Aa,H2-Eb1,H2-Ab1
DE_genes_HSC_TGR5_vs_MDR2KO Leishmaniasis KEGG:05140 4 70 0.0571 0.0403 Jun,H2-Aa,H2-Eb1,H2-Ab1
DE_genes_HSC_TGR5_vs_MDR2KO Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) REAC:R-MMU-381426 7 111 0.0631 0.00027 Spp1,Penk,Igfbp6,Gpc3,Ahsg,Ccn1,Igfbp3
DE_genes_HSC_TGR5_vs_MDR2KO Post-translational protein phosphorylation REAC:R-MMU-8957275 6 105 0.0571 0.00305 Spp1,Penk,Gpc3,Ahsg,Ccn1,Igfbp3
DE_genes_HSC_TGR5_vs_MDR2KO Innate Immune System REAC:R-MMU-168249 15 976 0.0154 0.00995 B2m,Ubc,H2-K1,Gsn,Clu,Jun,Ahsg,C7,Ttr,Hspa1a,Tyrobp,Lyz2,C1qb,C1qa,C1qc
DE_genes_HSC_TGR5_vs_MDR2KO Regulation of Complement cascade REAC:R-MMU-977606 5 99 0.0505 0.0316 Clu,C7,C1qb,C1qa,C1qc
DE_genes_HSC_TGR5_vs_MDR2KO Complement cascade REAC:R-MMU-166658 5 109 0.0459 0.0498 Clu,C7,C1qb,C1qa,C1qc
DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO Coronavirus disease - COVID-19 KEGG:05171 23 239 0.0962 6.04e-13 Fau,Rps15a,Rps11,Rpl32,Rpl27a,Rpl34,Rpl39,Rpl37,Rpl18a,Rps5,Rpl6,Rpl28,Rpl36,Rplp0,Nfkbia,Tnf,Il1b,Rps18,C8g,Fgb,C6,Cxcl10,Fgg
DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO Ribosome KEGG:03010 15 137 0.109 7.33e-09 Fau,Rps15a,Rps11,Rpl32,Rpl27a,Rpl34,Rpl39,Rpl37,Rpl18a,Rps5,Rpl6,Rpl28,Rpl36,Rplp0,Rps18
DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO NF-kappa B signaling pathway KEGG:04064 10 104 0.0962 4.22e-05 Gadd45b,Bcl2a1b,Cd14,Ccl4,Cxcl2,Nfkbia,Tnf,Il1b,Cxcl1,Icam1
DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO PPAR signaling pathway KEGG:03320 9 89 0.101 0.000106 Fabp1,Apoa2,Apoc3,Scp2,Scd1,Hmgcs2,Apoa1,Lpl,Dbi
DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO Complement and coagulation cascades KEGG:04610 9 91 0.0989 0.000128 Serpina1d,Serpina1c,Serpina1e,C8g,Serpina1a,Serpina1b,Fgb,C6,Fgg
DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO Viral protein interaction with cytokine and cytokine receptor KEGG:04061 9 92 0.0978 0.00014 Cx3cr1,Ccl4,Cxcl2,Tnf,Ccl3,Cxcl13,Cxcl1,Ccr2,Cxcl10
DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO Cholesterol metabolism KEGG:04979 7 49 0.143 0.000162 Apoa2,Apoe,Apoc3,Angptl3,Apoh,Apoa1,Lpl
DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO Rheumatoid arthritis KEGG:05323 8 84 0.0952 0.000667 Il1a,Cxcl2,Tnf,Acp5,Ccl3,Il1b,Cxcl1,Icam1
DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO Fluid shear stress and atherosclerosis KEGG:05418 9 141 0.0638 0.00459 Il1a,Tnf,Il1b,Mgst1,Ass1,Icam1,Gsta3,Cdh5,Gstm1
DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO Legionellosis KEGG:05134 6 60 0.1 0.00729 Cd14,Cxcl2,Nfkbia,Tnf,Il1b,Cxcl1
DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO IL-17 signaling pathway KEGG:04657 7 88 0.0795 0.00811 Cxcl2,Nfkbia,Tnf,Il1b,Cxcl1,Fosb,Cxcl10
DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO Toll-like receptor signaling pathway KEGG:04620 7 98 0.0714 0.016 Cd14,Ccl4,Nfkbia,Tnf,Ccl3,Il1b,Cxcl10
DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO Cytokine-cytokine receptor interaction KEGG:04060 12 287 0.0418 0.0163 Cx3cr1,Ccl4,Il1a,Cxcl2,Tnf,Ccl3,Cxcl13,Il1b,Cxcl1,Gdf15,Ccr2,Cxcl10
DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO Amoebiasis KEGG:05146 7 103 0.068 0.0218 Cd14,Cxcl2,Tnf,Il1b,Cxcl1,C8g,Arg1
DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO TNF signaling pathway KEGG:04668 7 109 0.0642 0.0309 Cxcl2,Nfkbia,Tnf,Il1b,Cxcl1,Icam1,Cxcl10
DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO Chemokine signaling pathway KEGG:04062 9 187 0.0481 0.039 Cx3cr1,Ccl4,Cxcl2,Nfkbia,Ccl3,Cxcl13,Cxcl1,Ccr2,Cxcl10
DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO Graft-versus-host disease KEGG:05332 5 55 0.0909 0.0456 Il1a,H2-T23,Tnf,Il1b,H2-Q10
DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO SRP-dependent cotranslational protein targeting to membrane REAC:R-MMU-1799339 12 89 0.135 8.62e-08 Rps15a,Rps11,Rpl32,Rpl27a,Rpl34,Rpl39,Rpl37,Rpl18a,Rpl6,Rpl28,Rplp0,Rps18
DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) REAC:R-MMU-975956 12 91 0.132 1.12e-07 Rps15a,Rps11,Rpl32,Rpl27a,Rpl34,Rpl39,Rpl37,Rpl18a,Rpl6,Rpl28,Rplp0,Rps18
DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO Formation of a pool of free 40S subunits REAC:R-MMU-72689 12 98 0.122 2.71e-07 Rps15a,Rps11,Rpl32,Rpl27a,Rpl34,Rpl39,Rpl37,Rpl18a,Rpl6,Rpl28,Rplp0,Rps18
DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO L13a-mediated translational silencing of Ceruloplasmin expression REAC:R-MMU-156827 12 108 0.111 8.48e-07 Rps15a,Rps11,Rpl32,Rpl27a,Rpl34,Rpl39,Rpl37,Rpl18a,Rpl6,Rpl28,Rplp0,Rps18
DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO GTP hydrolysis and joining of the 60S ribosomal subunit REAC:R-MMU-72706 12 109 0.11 9.44e-07 Rps15a,Rps11,Rpl32,Rpl27a,Rpl34,Rpl39,Rpl37,Rpl18a,Rpl6,Rpl28,Rplp0,Rps18
DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) REAC:R-MMU-975957 12 112 0.107 1.29e-06 Rps15a,Rps11,Rpl32,Rpl27a,Rpl34,Rpl39,Rpl37,Rpl18a,Rpl6,Rpl28,Rplp0,Rps18
DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO Nonsense-Mediated Decay (NMD) REAC:R-MMU-927802 12 112 0.107 1.29e-06 Rps15a,Rps11,Rpl32,Rpl27a,Rpl34,Rpl39,Rpl37,Rpl18a,Rpl6,Rpl28,Rplp0,Rps18
DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO Eukaryotic Translation Initiation REAC:R-MMU-72613 12 116 0.103 1.94e-06 Rps15a,Rps11,Rpl32,Rpl27a,Rpl34,Rpl39,Rpl37,Rpl18a,Rpl6,Rpl28,Rplp0,Rps18
DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO Cap-dependent Translation Initiation REAC:R-MMU-72737 12 116 0.103 1.94e-06 Rps15a,Rps11,Rpl32,Rpl27a,Rpl34,Rpl39,Rpl37,Rpl18a,Rpl6,Rpl28,Rplp0,Rps18
DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO Retinoid metabolism and transport REAC:R-MMU-975634 8 44 0.182 8.31e-06 Apoa2,Apoe,Sdc3,Akr1c6,Ttr,Apoa1,Rbp4,Lpl
DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO Metabolism of fat-soluble vitamins REAC:R-MMU-6806667 8 49 0.163 2.02e-05 Apoa2,Apoe,Sdc3,Akr1c6,Ttr,Apoa1,Rbp4,Lpl
DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO Metabolism REAC:R-MMU-1430728 42 1678 0.025 3.02e-05 Fabp1,Apoa2,Gnmt,Alb,Apoe,Car3,Acp5,Gchfr,Sdc3,Akr1c6,Fbp1,Adh1,Hpd,Scp2,Otc,Arg1,Aldob,Cyp3a11,Cdo1,Tdo2,Pcbd1,Mgst1,Stard10,Ttr,Ass1,Tst,Gc,Rida,Scd1,Gsta3,Hmgcs2,Aldh1a1,Apoa1,Rbp4,Phyh,Gamt,Lpl,Hilpda,Etfb,Acaa2,Dbi,Cyb5a
DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO Chemokine receptors bind chemokines REAC:R-MMU-380108 8 58 0.138 7.88e-05 Cx3cr1,Ccrl2,Ccl4,Cxcl2,Ccl3,Cxcl13,Cxcl1,Cxcl10
DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO Plasma lipoprotein remodeling REAC:R-MMU-8963899 6 25 0.24 8.59e-05 Apoa2,Alb,Apoe,Angptl3,Apoa1,Lpl
DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO rRNA processing REAC:R-MMU-72312 12 168 0.0714 0.000122 Rps15a,Rps11,Rpl32,Rpl27a,Rpl34,Rpl39,Rpl37,Rpl18a,Rpl6,Rpl28,Rplp0,Rps18
DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO Major pathway of rRNA processing in the nucleolus and cytosol REAC:R-MMU-6791226 12 168 0.0714 0.000122 Rps15a,Rps11,Rpl32,Rpl27a,Rpl34,Rpl39,Rpl37,Rpl18a,Rpl6,Rpl28,Rplp0,Rps18
DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO rRNA processing in the nucleus and cytosol REAC:R-MMU-8868773 12 168 0.0714 0.000122 Rps15a,Rps11,Rpl32,Rpl27a,Rpl34,Rpl39,Rpl37,Rpl18a,Rpl6,Rpl28,Rplp0,Rps18
DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO Translation REAC:R-MMU-72766 13 218 0.0596 0.00031 Rps15a,Rps11,Rpl32,Rpl27a,Rpl34,Rpl39,Rpl37,Rpl18a,Rpl6,Rpl28,Eef2,Rplp0,Rps18
DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO Chylomicron remodeling REAC:R-MMU-8963901 4 10 0.4 0.000971 Apoa2,Apoe,Apoa1,Lpl
DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO Plasma lipoprotein assembly, remodeling, and clearance REAC:R-MMU-174824 7 58 0.121 0.00116 Apoa2,Alb,Apoe,Angptl3,Apoc4,Apoa1,Lpl
DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO Metabolism of vitamins and cofactors REAC:R-MMU-196854 11 173 0.0636 0.00121 Apoa2,Apoe,Acp5,Gchfr,Sdc3,Akr1c6,Ttr,Apoa1,Rbp4,Lpl,Cyb5a
DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO Binding and Uptake of Ligands by Scavenger Receptors REAC:R-MMU-2173782 8 86 0.093 0.00168 Alb,Apoe,Marco,Cd163,Apoa1,Hp,Hpx,Ambp
DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO G alpha (i) signalling events REAC:R-MMU-418594 15 347 0.0432 0.00243 Apoa2,Cx3cr1,Rgs10,Apoe,Ccl4,Cxcl2,Sdc3,Akr1c6,Cxcl13,Cxcl1,Ttr,Cxcl10,Apoa1,Rbp4,Lpl
DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO Visual phototransduction REAC:R-MMU-2187338 8 91 0.0879 0.00257 Apoa2,Apoe,Sdc3,Akr1c6,Ttr,Apoa1,Rbp4,Lpl
DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO Platelet degranulation REAC:R-MMU-114608 8 110 0.0727 0.0104 Alb,Orm1,Cd63,Fgb,Apoh,Apoa1,Fgg,Ahsg
DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO Plasma lipoprotein assembly REAC:R-MMU-8963898 4 18 0.222 0.0132 Apoa2,Apoe,Apoc4,Apoa1
DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO Response to elevated platelet cytosolic Ca2+ REAC:R-MMU-76005 8 115 0.0696 0.0143 Alb,Orm1,Cd63,Fgb,Apoh,Apoa1,Fgg,Ahsg
DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO Metabolism of amino acids and derivatives REAC:R-MMU-71291 11 240 0.0458 0.0259 Gnmt,Hpd,Otc,Arg1,Cdo1,Tdo2,Pcbd1,Ass1,Tst,Rida,Gamt
DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO HDL remodeling REAC:R-MMU-8964058 3 9 0.333 0.0352 Alb,Apoe,Apoa1
DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO Scavenging by Class A Receptors REAC:R-MMU-3000480 3 9 0.333 0.0352 Apoe,Marco,Apoa1
DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO Urea cycle REAC:R-MMU-70635 3 10 0.3 0.0499 Otc,Arg1,Ass1
DE_genes_Macrophage_Kupffer_TGR5_vs_MDR2KO Chylomicron assembly REAC:R-MMU-8963888 3 10 0.3 0.0499 Apoa2,Apoe,Apoa1

2 Methods

For pathway analysis, the R package gprofiler2 v0.2.0 was employed. Graphs were produced in RStudio with R version 4.0.3 (2020-10-10) mainly using the R package ggplot2 v3.3.2. Final reports were produced using the R package rmarkdown v2.6, with knitr v1.30.